# Now, when you access the Jmol-utilizing website in question, the version of Jmol loaded in your web browser should be the same version being supplied by the server for the website. If this procedure is unclear, or fails to work, please contact emartz@microbio.umass.edu.

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# Now, when you access the Jmol-utilizing website in question, the version of Jmol loaded in your web browser should be the same version being supplied by the server for the website. If this procedure is unclear, or fails to work, please contact emartz AT microbio DOT umass DOT edu.

Java console

The Java console collects messages and errors during operation of Jmol. When something does not work (e.g. a file does not get loaded, or a script is not completed), that's a place to look for the source of trouble.

Note: the Java Console is different and separate from Jmol's script console.

Depending on your operating system and browser, the way to access the Java console varies. Here are some of the access routes:

Look for a Java icon (a cup of coffee) in Windows taskbar (lower right of the screen); right-click on it and choose Open Console (Firefox and Internet Explorer in Windows).

Java cache

Applets in web pages visited are cached by the browser into a Java cache space in local disk (different from the browser's cache). This allows a faster response when the same applet is used in another web page visited later.

However, on some occasions this may cause trouble. Namely, if you open a new web page that uses a different version of the Jmol applet, sometimes the browser will use the former applet version rather than the new one. In these cases, even closing and reopening the browser, or clearing the browser cache, may give no solution. Then, you will have to clear the Java cache manually.

To check the version of the Jmol applet being displayed in your web browser, click on the Jmol frank in the lower right corner (or right click in Jmol on Windows / ctrl click in Jmol on Mac OS X), then click on About Jmol.

If keep temporary files for fast access is not checked, the cache is disabled. If it is checked, continue.

Click the button Delete Files.

In the confirmation dialog, make sure that Applications and Applets is checked.

Click OK.

Clearing the Java Cache Using OS X Terminal

In unusual cases, the procedure in the previous section fails to clear the Jmol applet from the Java cache in Mac OS X. This has been observed when the version of Jmol was rolled back to an earlier version at Proteopedia.Org.

The following procedure should only be attempted if you are confident that you can do it correctly. Errors in this procedure could inadvertently erase programs or data! Commands must be typed very carefully without errors. Back up your system before proceeding!

MacOS X (this is known to apply to Java 1.5.0_20 in OS 10.5.8)

Print these instructions, or copy them into a text program such as iWork Pages or MS Word, so you will have them available after the browser is closed.

Quit your web browser(s), such as Safari, Firefox, Camino, etc.

In Java Preferences (see previous section for how to open it), note the location where temporary files are kept. Typically, this will be /Users/your_account/Library/Caches/Java/cache. If it is different, you will need to modify the following steps accordingly.

Open Terminal (Applications, Utilities, double click Terminal.app).

Type the following command in Terminal, in order to change to the Caches directory: cd /Users/your_account/Library/Caches, making sure to change your_account to your actual account name. Press Enter.

Confirm that you are now in Caches by typing pwd (print working directory) in Terminal, and pressing Enter. The report should be /Users/your_account/Library/Caches. If it is not, repeat the previous step.

Type the following command in Terminal: find . -iname jmolapplet*. Note the space-period-space between find and -iname, the hyphen before iname, and that there is no space between jmolapplet and *. These are critical. Press Enter.

Note the directories in which JmolApplet* files are reported, such as ./Java/cache/javapi/v1.0/jar.

Change to the first directory in which JmolApplet files are reported, for example cd ./Java/cache/javapi/v1.0/jar.

Confirm that you are in the desired directory using pwd, for example /Users/emartz/Library/Caches/Java/cache/javapi/v1.0/jar. DO NOT PROCEED IF THERE IS ANY DOUBT.

Delete the applet files by typing this command in Terminal: rm -v JmolApplet*. Note that J and A must be capitalized in JmolApplet, and that there is no space before the *.

If more than one directory was reported earlier by the find command, repeat the above steps to delete JmolApplet files in each directory that contains them.

Quit Terminal.

Restart your computer.

Now, when you access the Jmol-utilizing website in question, the version of Jmol loaded in your web browser should be the same version being supplied by the server for the website. If this procedure is unclear, or fails to work, please contact emartz AT microbio DOT umass DOT edu.

Diagnosing Java - Javascript communication

This is a useful page for testing communication between Java applets and Javascript.

Google Chrome browser

This web browser (released Sept. 2008) is only compatible with Java version 6u10 (also named 1.6.0_10), or later. If the browser is up-to-date, it should direct you to the adequate download page automatically whenever you try a page with an applet. If not, search Sun's Java site for this version (currently in beta, or Release Candidate state), or go to full listing of Java downloads.